GSM7384512: ChIPseq_mESC_hIDR2_YY1_Input_R2; Mus musculus; ChIP-Seq
ChIP was performed as previously described (Lee et al., 2006). Briefly, 5×107 –1×108 ESCs were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125mM glycine. Rinsed cells twice with ice cold PBS and then resuspended in Lysis Buffer with protease inhibitor. Chromatin was sonicated into 200–500bp range. Dynabeads (Invitrogen 10004D) pre-blocked with 0.5% BSA were incubated with 10μg antibody for more than 8 hours. Chromatin was added to antibody-bead complex and incubated rotating overnight at 4°C.Beads were washed with each of the following buffers: Wash Buffer (RIPA), TE + 50 mM NaCl at 4°C, followed by washing one time with TE at room temperature. Chromatin were eluted by incubating at 65°C for 45min in elution buffer. Reversal of crosslinking was performed at 65°C overnight. After treated with 10 mg/ml RNaseA and 20 mg/ml proteinase K. DNA fragments were then purified using phenol–chloroform extraction and resuspended in 10mM Tris-HCL. The antibodies were:  JMJD2/KDM4A Bethyl A300-861A, anti-H3K27ac Abcam ab4729, anti-H3K9me3 Abcam ab8898 and anti-YY1 Abcam ab109237.